[English] 日本語
Yorodumi- PDB-6itf: Icosahedral asymmetric unit (iASU) model of the less refined, coa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6itf | ||||||
---|---|---|---|---|---|---|---|
Title | Icosahedral asymmetric unit (iASU) model of the less refined, coarse part of FHV eluted particle | ||||||
Components | CAPSID PROTEIN BETA | ||||||
Keywords | VIRUS / Flock House Virus / Disassembly intermediate / Asymmetric reconstruction | ||||||
Function / homology | Function and homology information nodavirus endopeptidase / symbiont entry into host cell via permeabilization of inner membrane / permeabilization of host organelle membrane involved in viral entry into host cell / T=3 icosahedral viral capsid / aspartic-type endopeptidase activity / proteolysis / metal ion binding Similarity search - Function | ||||||
Biological species | Flock house virus | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 Å | ||||||
Authors | Banerjee, M. / Azad, K. | ||||||
Funding support | India, 1items
| ||||||
Citation | Journal: J Virol / Year: 2019 Title: Structural Dynamics of Nonenveloped Virus Disassembly Intermediates. Authors: Kimi Azad / Manidipa Banerjee / Abstract: The stability of icosahedral viruses is crucial for protecting the viral genome during transit; however, successful infection requires eventual disassembly of the capsid. A comprehensive ...The stability of icosahedral viruses is crucial for protecting the viral genome during transit; however, successful infection requires eventual disassembly of the capsid. A comprehensive understanding of how stable, uniform icosahedrons disassemble remains elusive, mainly due to the complexities involved in isolating transient intermediates. We utilized incremental heating to systematically characterize the disassembly pathway of a model nonenveloped virus and identified an intriguing link between virus maturation and disassembly. Further, we isolated and characterized two intermediates by cryo-electron microscopy and three-dimensional reconstruction, without imposing icosahedral symmetry. The first intermediate displayed a series of major, asymmetric alterations, whereas the second showed that the act of genome release, through the 2-fold axis, is actually confined to a small section on the capsid. Our study thus presents a comprehensive structural analysis of nonenveloped virus disassembly and emphasizes the asymmetric nature of programmed conformational changes. Disassembly or uncoating of an icosahedral capsid is a crucial step during infection by nonenveloped viruses. However, the dynamic and transient nature of the disassembly process makes it challenging to isolate intermediates in a temporal, stepwise manner for structural characterization. Using controlled, incremental heating, we isolated two disassembly intermediates: "eluted particles" and "puffed particles" of an insect nodavirus, Flock House virus (FHV). Cryo-electron microscopy and three-dimensional reconstruction of the FHV disassembly intermediates indicated that disassembly-related conformational alterations are minimally global and largely local, leading to asymmetry in the particle and eventual genome release without complete disintegration of the icosahedron. | ||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6itf.cif.gz | 106.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6itf.ent.gz | 78.6 KB | Display | PDB format |
PDBx/mmJSON format | 6itf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6itf_validation.pdf.gz | 1007.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6itf_full_validation.pdf.gz | 1017.2 KB | Display | |
Data in XML | 6itf_validation.xml.gz | 26.8 KB | Display | |
Data in CIF | 6itf_validation.cif.gz | 38.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/it/6itf ftp://data.pdbj.org/pub/pdb/validation_reports/it/6itf | HTTPS FTP |
-Related structure data
Related structure data | 9730MC 9732C 6itbC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
| x 60
2 |
|
3 |
| x 5
4 |
| x 6
5 |
|
Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 39367.355 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Flock house virus / Gene: alpha / Cell line (production host): DL-1 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P12870, nodavirus endopeptidase |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Flock house virus / Type: VIRUS Details: Purified wildtype Flock House Virus heated to 70 degC Entity ID: all / Source: RECOMBINANT |
---|---|
Molecular weight | Value: 9 MDa / Experimental value: YES |
Source (natural) | Organism: Flock house virus |
Source (recombinant) | Organism: Drosophila melanogaster (fruit fly) |
Details of virus | Empty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION |
Natural host | Organism: Costelytra zealandica |
Virus shell | Diameter: 300 nm / Triangulation number (T number): 3 |
Buffer solution | pH: 7 |
Buffer component | Conc.: 50 mM / Name: HEPES / Formula: C8H18N2O4S |
Specimen | Conc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Purified wildtype Flock House Virus heated to 70 degC |
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 284 K / Details: Blot for 3 seconds before plunging |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 5 sec. / Electron dose: 20 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 2835 |
EM imaging optics | Energyfilter name: GIF Quantum LS |
Image scans | Movie frames/image: 40 |
-Processing
EM software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 61905 / Details: Manual selection | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 58918 / Algorithm: FOURIER SPACE / Num. of class averages: 30 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | B value: 181 / Protocol: OTHER / Space: REAL | ||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 4FTB Accession code: 4FTB / Source name: PDB / Type: experimental model |